Imho you should not put any Fuzz/OD in the FX Loop, nor any other pedal that is supposed to drive and boost a signal. That's a rule I personally follow since day one, and I do really believe it's related to I/O circuits at the ports, so nothing you can change software side. Even the most clean clone of Klone pedal I put the in the Loop sounds noisy, and also it does work differently then when it's running in front (as it should, imho).
Personally, the only real downside of the loops, is they do suck a bit of tone, which is most evident with clean sounds, but it's always a compromise I guess. :)
EDIT; added "IMHO" to prevent sensible people to feel offended.